|
|
ad8de80353
|
Views: better checks when adding an existing column to a view
|
2017-04-06 14:44:07 +02:00 |
|
|
|
8cd3e3604f
|
Cython Column API
|
2017-04-06 14:42:11 +02:00 |
|
|
|
255f3c92ae
|
Cython View API
|
2017-04-06 14:41:58 +02:00 |
|
|
|
08be4e231d
|
Cython Object API
|
2017-04-06 14:41:43 +02:00 |
|
|
|
b5b7995411
|
new Cython DMS API
|
2017-04-06 14:41:26 +02:00 |
|
|
|
0dfb1eb3e6
|
Cython typed columns
|
2017-04-06 14:40:44 +02:00 |
|
|
|
381194194c
|
Cython API: compiling but not working
|
2017-03-06 16:07:02 +01:00 |
|
|
|
778acc48cd
|
Added linked lists to handle lists of column pointers in views (not
tested)
|
2017-03-06 16:06:17 +01:00 |
|
|
|
3319ede837
|
Views: Column dictionaries now store and return pointers on column
pointers instead of column pointers.
|
2017-02-22 13:49:50 +01:00 |
|
|
|
fc20b83ad1
|
Merging
|
2017-02-20 14:56:04 +01:00 |
|
|
|
431c1c8c6a
|
Merge branch 'Eric_new_Python_API' of
git@git.metabarcoding.org:obitools/obitools3.git into
Eric_new_Python_API
Conflicts:
python/obitools3/obidms/_obidms.pxd
python/obitools3/obidms/_obidms.pyx
python/obitools3/obidms/_obidmscolumn_bool.pyx
python/obitools3/obidms/_obidmscolumn_str.pyx
python/obitools3/obidms/_obiseq.pxd
python/obitools3/obidms/_obiseq.pyx
python/obitools3/obidms/_obitaxo.pxd
python/obitools3/obidms/_obitaxo.pyx
python/obitools3/obidms/_obiview.pxd
python/obitools3/obidms/_obiview.pyx
python/obitools3/obidms/_obiview_nuc_seq.pxd
python/obitools3/obidms/_obiview_nuc_seq.pyx
python/obitools3/obidms/_obiview_nuc_seq_qual.pxd
python/obitools3/obidms/_obiview_nuc_seq_qual.pyx
python/obitools3/obidms/capi/obialign.pxd
python/obitools3/obidms/capi/obidmscolumn.pxd
python/obitools3/obidms/capi/obitaxonomy.pxd
python/obitools3/obidms/capi/obiview.pxd
|
2017-02-20 14:55:36 +01:00 |
|
|
|
f23315e26f
|
New Cython API: compile but doesn't work
|
2017-02-17 15:14:06 +01:00 |
|
|
|
071a3b61ab
|
Merged master fixed conflict.
|
2017-02-14 10:58:43 +01:00 |
|
|
|
e524041013
|
Views: Files for unfinished views now have the extension
'.obiview_unfinished', renamed to '.obiview' when the view is finished.
|
2017-02-07 17:16:09 +01:00 |
|
|
|
a9102620f5
|
Fixed missing email address
|
2017-02-07 17:14:10 +01:00 |
|
|
|
7e9932f488
|
Fixed a C function declaration
|
2017-02-07 17:12:56 +01:00 |
|
|
|
e50da64ea1
|
The elements names when a column contains several elements per line are
now formatted with '\0' as separator and handled in a more optimized way
|
2017-01-31 16:48:06 +01:00 |
|
|
|
651c1d7845
|
utilities: bsearch and qsort with additional user_data pointer argument
|
2017-01-31 16:45:47 +01:00 |
|
|
|
c0bcdce724
|
Taxonomy: documentation for all the functions, and fixed bugs when
closing the taxonomy (overwriting of .pdx files, missing freeing, and
re-placed a misplaced condition)
|
2017-01-18 18:22:49 +01:00 |
|
|
|
c065c1914a
|
Taxonomy: adding, writing and reading preferred names, changed some
function names, and fixed a bug with taxa indices not being properly
initialized
|
2017-01-16 17:28:20 +01:00 |
|
|
|
0385a92e02
|
Taxonomy: Refactored the taxdump reading, and little fixes
|
2017-01-11 16:36:08 +01:00 |
|
|
|
cf7f2de016
|
Modify __init__ and close method to deal with registration process
|
2017-01-10 14:26:16 +01:00 |
|
|
|
5122ad52a7
|
Merge branch 'Eric_new_Python_API' of git@git.metabarcoding.org:obitools/obitools3.git into Eric_new_Python_API
|
2017-01-10 14:07:50 +01:00 |
|
|
|
4b02ba73ac
|
Add the OBIObject concept
|
2017-01-10 14:07:10 +01:00 |
|
|
|
41ad3deec0
|
Taxonomy: informations about deleted taxids is now read from
delnodes.dmp file and added to *.adx file
|
2017-01-09 17:28:49 +01:00 |
|
|
|
d68374018b
|
Taxonomy: functions to read the *.adx file (containing the deprecated
and current taxids and their corresponding indices in the taxa
structure) and to find the taxa using the merged index.
|
2017-01-06 15:52:21 +01:00 |
|
|
|
f396625f98
|
Taxonomy: function to write *.adx files
|
2017-01-05 15:37:13 +01:00 |
|
|
|
897032387f
|
Taxonomy: reading merged.dmp file in taxdump
|
2017-01-05 14:28:36 +01:00 |
|
|
|
4a1d3167a7
|
Last change on my branch
|
2017-01-02 16:46:52 +01:00 |
|
|
|
153c22257f
|
Last change on my branch
|
2017-01-02 16:46:17 +01:00 |
|
|
|
2139bfc748
|
refactoring...
|
2017-01-02 13:05:22 +01:00 |
|
|
|
65f3b16e6d
|
Refactoring ...
|
2016-12-29 18:22:05 +01:00 |
|
|
|
0526386337
|
first working DMS class
|
2016-12-27 06:17:45 +01:00 |
|
|
|
62caf1346e
|
temporary remove some files
|
2016-12-26 15:03:24 +01:00 |
|
|
|
3ac6e85fb3
|
Big refactoring 4
|
2016-12-26 14:58:03 +01:00 |
|
|
|
5156f6bb9e
|
Big refactoring 3
|
2016-12-26 14:18:01 +01:00 |
|
|
|
e6db2086d5
|
Big refactoring 2
|
2016-12-26 13:56:31 +01:00 |
|
|
|
daacd0df76
|
Strong refactoring 1
|
2016-12-26 13:35:31 +01:00 |
|
|
|
8e92bf6dac
|
LCS alignment: it is now checked that sequences are not longer than what
a 16 bits integer can code for (as the LCS and alignment lengths are
kept in 16 bits registers)
|
2016-12-22 17:06:23 +01:00 |
|
|
|
30e4359c85
|
LCS alignment: documentation for all the lowest level functions
|
2016-12-22 17:03:51 +01:00 |
|
|
|
5c50e5b378
|
Embryo of code for openMP parallelization of LCS alignment but
deactivated for now because can't make it compile with cython/clang
|
2016-12-20 11:46:58 +01:00 |
|
|
|
3cedd00d7f
|
Add register function for column type
|
2016-12-20 11:13:57 +01:00 |
|
|
|
82fbe43980
|
transfert method to obiviews
|
2016-12-20 08:18:47 +01:00 |
|
|
|
d1a972dfcb
|
patch import
|
2016-12-20 08:15:42 +01:00 |
|
|
|
f43dc3e3ab
|
separate the obicolumn classes in new files
|
2016-12-20 08:15:08 +01:00 |
|
|
|
9c71b06117
|
Removed deprecated TODOs
|
2016-12-19 14:36:40 +01:00 |
|
|
|
3bf5260174
|
Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git
|
2016-12-19 10:31:18 +01:00 |
|
|
|
857a5198e4
|
Updated `obi lcs` for the LCS alignment of two columns
|
2016-12-16 19:40:36 +01:00 |
|
|
|
d99447c12b
|
C function for LCS alignment of two columns, and optimized and fixed
line count bug in function to align one column
|
2016-12-16 19:39:02 +01:00 |
|
|
|
303bd6f445
|
Added function to build kmer table for 2 columns, and fixed bug (with
line count) when building kmer table of one column
|
2016-12-16 19:10:18 +01:00 |
|
